[gmx-users] Re: g_msd with input by trjconv -pbc nojump:a concern

Tue Mar 20 12:37:09 CET 2012

On Tue, 2012-03-20 at 11:38 +0200, Ioannis Beis wrote: 
> > Message: 3
> > Date: Mon, 19 Mar 2012 15:05:43 +0100
> > From: Dommert Florian <dommert at icp.uni-stuttgart.de>
> > Subject: Re: [gmx-users] g_msd with input by trjconv -pbc nojump:a
> > 	concern
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <1332165943.4071.82.camel at fermi>
> > Content-Type: text/plain; charset="utf-8"
> 
> Hi and thanks for the reply!
> 
> >
> > Hi,
> >
> > perhaps this problem is related to bug 774:
> >
> > http://redmine.gromacs.org/issues/774
> 
> The destination exhibits internal server error, thus I don't have access.
> 
> >
> > which has been discussed quite often, recently. Somehow there is a
> > problem in the order of removing the PBC and jumps. As already
> > mentioned, I could solve the problem by providing a trajectory with
> > whole molecules to g_msd. An indexfile with seperate groups for every
> > molecule has to be created and finally every single molecule group has
> > to be analyzed, but WITHOUT the -mol flag. Afterwards the resulting MSDs
> > only need to be averaged.
> 
> I used trjconv first with nojump and I used this as input for a  
> subsequent trjconv with mol.

Hi,

I would not use nojump, because g_msd seems to deal with this correctly,
but -pbc whole, perhaps this can solve this problem.

/Flo

> I suppose that's what you mean by  
> "providing a trajectory with whole molecules to g_msd". Then I issued  
> g_msd without -mol, providing as index all the atoms of the under  
> interest molecule. The results are still bad. Am I doing something  
> wrong still?
> 
> Apart from this (which is an additional concern as it seems), my  
> initial question was mostly about whether or not .xtc files carry all  
> information about jumps in addition to coordinates. If the frequency  
> of saving is small, then it might be possible for a molecule to be in  
> two consecutive frames whole, but in the inbetween time it might have  
> jumped. Can trjconv -pbc nojump capture this event? Or is it aware  
> only if it sees the molecule crossing at the very moment of the frame?
> 
> If the second case is true, then this can have fatal consequencies to  
> MSD calculations. An extreme example: if a molecule moves along 1D in  
> a box that has corresponding vector of length a and between two frames  
> moves by a, then one case gives rise to displacement of a and the  
> other of 0.
> 
> I would appreciate if someone let me know whether -pbc nojump  
> continuity is unconditional or frequency of saving-dependent.
> 
> Thank you in advance!
> 
> Best regards,
> Ioannis
> 
> >
> > /Flo
> >
> >
> > On Mon, 2012-03-19 at 14:31 +0200, Ioannis Beis wrote:
> >> Dear Gromacs users,
> >>
> >> I have been trying to calculate the lateral MSD of lipid molecules
> >> within a bilayer. I have performed simulations in a rectangular box
> >> with PBC. I have used trjconv with -pbc nojump. I compared results
> >> between the initial trajectory and the one generated by trjconv for 6
> >> different lipids. In 5 cases the calculated MSD was identical and only
> >> in one there was difference (big difference). According to the
> >> results, MSD loses linearity and exhibits large fluctuations after
> >> some point. The above give rise to the following concern.
> >>
> >> As far as I understand, -pbc nojump checks if any molecule crosses the
> >> box boundaries and if yes it brings back the broken part from the
> >> symmetric side to the original place, keeping the molecule whole. This
> >> way box information is lost, but each molecule is supposed to have
> >> continuous trajectories. The true continuity of trajectories, however,
> >> is only secured only if .xtc files carry all information of boundary
> >> crosses based on the time step of the initial run in addition to all
> >> coordinates for all times. Otherwise, the result is clearly dependent
> >> on the frequency of saving and continuity is not guaranteed.
> >>
> >> E.g. in my case -I have small frequency of saving (100 ps) for long
> >> simulations to avoid very large output files- one can't tell based
> >> merely on the coordinates whether or not a lipid crossed boundaries
> >> between two consecutive frames. Of course if the lipid went back and
> >> forth then the result of the calculation would  not be affected but
> >> only by statistical means; however if the lipid had an overall
> >> translation across the box (not captured by -pbc nojump because the
> >> molecule is whole in both frames), then the calculation is destroyed.
> >>
> >> If this is the case, it seems to me that g_msd might in practice give
> >> correct results for proteins, but for smaller molecules the
> >> reliability of the results depends sensitively on molecule
> >> size-frequency of saving coordinates relationship and might give rise
> >> to huge systematic errors.
> >>
> >> Is there a way to obtain a converted trajectory that guarantees
> >> unconditional continuity, so that one makes sure that he obtains the
> >> proper MSD for his molecules?
> >>
> >> Thank you in advance!
> >>
> >> Best regards,
> >> Ioannis
> >>
> >>
> >
> > --
> > Florian Dommert
> > Dipl. - Phys.
> >
> > Institute for Computational Physics
> > University Stuttgart
> >
> > Pfaffenwaldring 27
> > 70569 Stuttgart
> >
> > EMail: dommert at icp.uni-stuttgart.de
> > Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
> >
> > Tel.: +49 - (0)711 - 68563613
> > Fax.: +49 - (0)711 - 68563658
> > -------------- next part --------------
> > A non-text attachment was scrubbed...
> > Name: not available
> > Type: application/pgp-signature
> > Size: 198 bytes
> > Desc: This is a digitally signed message part
> > Url :   
> > http://lists.gromacs.org/pipermail/gmx-users/attachments/20120319/bf0fbf11/attachment-0001.bin
> >
> 

-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 198 bytes
Desc: This is a digitally signed message part
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120320/066069d9/attachment.sig>